Cédric Raguenaud

A model for representing taxonomic descriptive data is presented. The model has been developed in response to the growing requirement for the global exchange of descriptive data. Meaningful exchange of data requires that data be represented in a form that can be consistently parsed and interpreted, requiring a common data model and the constrained...

Taxonomists classify biological specimens into groups (taxa) on the basis of similarities between their observed features ('characters'). The descrip- tion of these 'characters' is therefore central to taxonomy, but there is currently no agreed model, defined terminology nor methodology for composing these descriptions. This lack of a common concep...

Taxonomy has been described as "the science of documenting biodiversity", which involves collecting, naming, describing, identifying and classifying specimens of organisms (Keogh, 1995). Descriptions are the fundamental information units used in the process of constructing classifications and communi-cating taxonomic concepts. The quality of stored...

Types of databases commonly used for handling taxonomic data are compared. It is shown that none of the existing types of databases fully support the requirements of taxonomic data. The results of this comparison provide a rationale for the design and implementation of a new database system based on an Extended Object- Oriented model. The new model...

This paper discusses issues and solutions for supporting multiple overlapping classifications in database systems. These classifications are commonly found in science, although they are often ignored in computing applications for scientific data, and inappropriate solutions adopted as their replacement. Known database models and classification tech...

A model for improving the storage and communication of plant descriptions is presented. The model is flexible and yet reduces the ambiguity often present in text descriptions. The fundamental idea behind the model is the necessity for clear representation of the meaning of each term used within a description. The model therefore emphasises the assi...

This paper analyses the problem generated by recursive patterns in typed query languages such as OQL [Cattell '97]. Recursive patterns describe hierarchical structures such as those defining classifications or part-explosion problems. A classification is composed of hierarchies of classes that eventually classify non-class objects. A part-explosion...

One of the tasks of plant taxonomy is the creation of classifications of organisms that allows the understanding of the evolutionary relationships between them. In this paper, we describe two different data models that have been designed to support two aspects of taxonomic work: the storage of the information and the visualisation of that informati...

One of the tasks of plant taxonomy is the creation of classifications of organisms that allows the understanding of the evolutionary relationships between them. In this paper we describe two different data models that have been designed to support two aspects of taxonomic work: the storage of the information and the visualisation of that informatio...

Introduction Taxonomists in the Royal Botanic Garden, Edinburgh, specialise in the classification of flora from around the world. The classification of flora is a complex task involving historical records, literature references and specimens collected from the field. Using this information the taxonomists formulate classifications which are continu...

Pullan, M. R., Watson, M. F., Kennedy, J. B., Raguenaud, C. & Hyam, R.: The Prometheus Taxonomic Model: a practical approach to representing multiple classifications. – Taxon 49: 55‐75. 2000. – ISSN 0040‐0262. A model for representing taxonomic data in a flexible and dynamic system capable of handling and comparing multiple simultaneous classificat...

This paper presents the work carried out in the Prometheus project and its motivation, taxonomy. Taxonomy presents challenges to common database systems. Because of its complexity and the necessary treatments applied to its data, common database model such as the relational, the object-oriented of even graph models are not able to support taxonomic...

M.R. Pullen et al. (2000) have designed a new model of plant taxonomy (called Prometheus); it supports multiple overlapping classifications, and distinguishes the process of naming from classifying. The concepts identified in this taxonomic model necessitated the design of a new database model - the Prometheus Object-Oriented Model (POOM) - to repr...

This paper draws on concepts from the structuralist analysis of narrative to explore aspects of the role of stories in the small group design process. A brief review of relevant narratological concepts is provided. Their application in a preliminary analysis of case study data from a team designing taxonomic software is then reported. It is conclud...

Summary Pullan, M.R., Watson, M.F., Kennedy, J.B., Raguenaud, C. & taxonomic concepts than purely descriptive circumscriptions , and is more explicit than merely providing pointers to where circumscriptions have been published. Using specimens as the fundamental elements of taxon circumscription also allows for the automatic naming of taxa based up...

Taxonomists classify organisms in order to refer to, identify and understand them. Over time, the same organism may be classified according to different taxonomic opinions. As alternative classifications multiply, taxonomists are faced with the need to compare and contrast taxonomies to identify how they differ. A taxonomy is hierarchical and multi...

Complex applications such as those to support the emerging field of biodiversity informatics, require database systems able to represent and manipulate their data. Object-oriented databases (OODBs), designed to support complex domains such as Computer Aided Engineering, appear to be a solution. A criticism of early OODBs was the lack of an ad hoc q...

This paper analyses the problem generated by recursive patterns in typed query languages such as OQL (Cattell '97). Recursive patterns describe hierarchical structures such as those defining classifications or part- explosion problems. A classification is composed of hierarchies of classes that eventually classify non-class objects. A part-explosio...

A criticism of early object-oriented databases (OODBs) was the lack of an ad hoc query language such as SQL. This led to the development of OQL (CBB+97), a generic ad hoc query language without domain specific operators. However OQL does not take advantage of the semantics which OODBs can capture, and thereby provides little more power than SQL. Th...